PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8051-8100 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | SNP | * | HG002complexvar | * | 99.9538 | 99.9332 | 99.9744 | 19.0217 | 753877 | 504 | 753722 | 193 | 84 | 43.5233 | |
| bgallagher-sentieon | INDEL | D6_15 | * | homalt | 98.4421 | 99.8893 | 97.0362 | 55.3606 | 6319 | 7 | 6319 | 193 | 190 | 98.4456 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.4618 | 99.9203 | 95.1213 | 59.6779 | 3763 | 3 | 3763 | 193 | 190 | 98.4456 | |
| ckim-gatk | SNP | * | map_l150_m0_e0 | * | 72.2501 | 57.4634 | 97.2832 | 92.5200 | 6914 | 5118 | 6911 | 193 | 26 | 13.4715 | |
| cchapple-custom | INDEL | D16_PLUS | * | * | 96.3496 | 95.5041 | 97.2102 | 62.8743 | 6479 | 305 | 6725 | 193 | 158 | 81.8653 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.7734 | 92.6190 | 94.9569 | 54.7101 | 3639 | 290 | 3634 | 193 | 182 | 94.3005 | |
| jmaeng-gatk | SNP | ti | map_l125_m0_e0 | * | 77.0171 | 63.5715 | 97.6758 | 88.7194 | 8113 | 4649 | 8111 | 193 | 22 | 11.3990 | |
| jli-custom | SNP | * | map_l125_m2_e0 | het | 99.0801 | 98.8232 | 99.3382 | 70.5778 | 28973 | 345 | 28970 | 193 | 54 | 27.9793 | |
| jli-custom | SNP | * | map_l125_m2_e1 | het | 99.0901 | 98.8360 | 99.3454 | 70.6523 | 29295 | 345 | 29292 | 193 | 54 | 27.9793 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002complexvar | homalt | 93.6134 | 89.6018 | 98.0010 | 59.6110 | 9496 | 1102 | 9462 | 193 | 170 | 88.0829 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 19.0690 | 11.4688 | 56.5315 | 43.2950 | 57 | 440 | 251 | 193 | 191 | 98.9637 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | het | 91.7425 | 85.6452 | 98.7744 | 60.7292 | 15578 | 2611 | 15555 | 193 | 126 | 65.2850 | |
| gduggal-snapvard | INDEL | * | map_l250_m1_e0 | * | 77.4944 | 91.1475 | 67.3986 | 95.4162 | 278 | 27 | 399 | 193 | 44 | 22.7979 | |
| gduggal-snapvard | INDEL | I1_5 | * | homalt | 92.2555 | 85.9022 | 99.6235 | 34.4127 | 51909 | 8519 | 51074 | 193 | 178 | 92.2280 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.0952 | 98.5606 | 95.6726 | 86.1499 | 4177 | 61 | 4267 | 193 | 28 | 14.5078 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5764 | 98.1511 | 99.0054 | 69.1058 | 19217 | 362 | 19211 | 193 | 36 | 18.6528 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5764 | 98.1511 | 99.0054 | 69.1058 | 19217 | 362 | 19211 | 193 | 36 | 18.6528 | |
| jlack-gatk | INDEL | * | map_l125_m1_e0 | * | 94.7690 | 98.2914 | 91.4903 | 90.0770 | 2071 | 36 | 2075 | 193 | 12 | 6.2176 | |
| jlack-gatk | INDEL | D1_5 | map_siren | * | 96.8891 | 99.0932 | 94.7810 | 83.4660 | 3497 | 32 | 3505 | 193 | 13 | 6.7358 | |
| hfeng-pmm2 | SNP | ti | map_l125_m2_e1 | * | 99.4245 | 99.4799 | 99.3693 | 73.2743 | 30410 | 159 | 30406 | 193 | 23 | 11.9171 | |
| hfeng-pmm2 | INDEL | D6_15 | * | * | 98.0668 | 96.9186 | 99.2426 | 51.7103 | 25288 | 804 | 25288 | 193 | 170 | 88.0829 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e0 | * | 99.6651 | 99.5917 | 99.7386 | 65.1842 | 73662 | 302 | 73651 | 193 | 31 | 16.0622 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.7416 | 95.5607 | 95.9231 | 39.1360 | 4542 | 211 | 4541 | 193 | 74 | 38.3420 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.9360 | 95.2617 | 96.6200 | 68.1344 | 5569 | 277 | 5517 | 193 | 187 | 96.8912 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.9360 | 95.2617 | 96.6200 | 68.1344 | 5569 | 277 | 5517 | 193 | 187 | 96.8912 | |
| ghariani-varprowl | INDEL | * | map_l150_m2_e1 | * | 90.7203 | 94.0931 | 87.5809 | 95.3621 | 1354 | 85 | 1354 | 192 | 56 | 29.1667 | |
| gduggal-snapplat | INDEL | * | map_l125_m2_e1 | * | 81.5919 | 74.4270 | 90.2834 | 93.4615 | 1656 | 569 | 1784 | 192 | 25 | 13.0208 | |
| jmaeng-gatk | SNP | ti | map_l125_m0_e0 | het | 80.4521 | 68.8612 | 96.7347 | 90.5884 | 5690 | 2573 | 5688 | 192 | 21 | 10.9375 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.0939 | 98.2086 | 96.0042 | 48.3222 | 4605 | 84 | 4613 | 192 | 8 | 4.1667 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 47.1967 | 32.7646 | 84.3521 | 58.6869 | 1037 | 2128 | 1035 | 192 | 177 | 92.1875 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.0342 | 97.2312 | 98.8506 | 67.1730 | 16505 | 470 | 16513 | 192 | 4 | 2.0833 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.0342 | 97.2312 | 98.8506 | 67.1730 | 16505 | 470 | 16513 | 192 | 4 | 2.0833 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9904 | 93.0008 | 95.0013 | 54.6571 | 3654 | 275 | 3649 | 192 | 181 | 94.2708 | |
| ckim-gatk | SNP | * | map_l150_m0_e0 | het | 75.5141 | 62.1285 | 96.2515 | 93.6797 | 4933 | 3007 | 4930 | 192 | 25 | 13.0208 | |
| eyeh-varpipe | SNP | ti | func_cds | * | 99.2850 | 99.9637 | 98.6154 | 24.7463 | 13782 | 5 | 13675 | 192 | 1 | 0.5208 | |
| eyeh-varpipe | SNP | ti | func_cds | het | 98.8564 | 99.9647 | 97.7724 | 26.7528 | 8501 | 3 | 8427 | 192 | 1 | 0.5208 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 94.3163 | 93.0341 | 95.6344 | 40.1307 | 3793 | 284 | 4206 | 192 | 187 | 97.3958 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 79.6904 | 73.7069 | 86.7312 | 40.6237 | 342 | 122 | 1255 | 192 | 190 | 98.9583 | |
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3936 | 99.8748 | 98.9170 | 66.2587 | 17546 | 22 | 17536 | 192 | 15 | 7.8125 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e0 | het | 85.8634 | 75.7005 | 99.1784 | 83.8574 | 23181 | 7441 | 23176 | 192 | 12 | 6.2500 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e1 | het | 85.9506 | 75.8301 | 99.1886 | 83.8404 | 23477 | 7483 | 23472 | 192 | 12 | 6.2500 | |
| ndellapenna-hhga | SNP | ti | HG002complexvar | homalt | 99.8705 | 99.8403 | 99.9007 | 18.4130 | 193154 | 309 | 193175 | 192 | 171 | 89.0625 | |
| hfeng-pmm3 | INDEL | I6_15 | * | homalt | 98.2839 | 99.5993 | 97.0028 | 48.9358 | 6214 | 25 | 6214 | 192 | 191 | 99.4792 | |
| hfeng-pmm2 | SNP | ti | map_l125_m2_e0 | * | 99.4203 | 99.4745 | 99.3661 | 73.2412 | 30099 | 159 | 30095 | 192 | 23 | 11.9792 | |
| jlack-gatk | INDEL | * | map_l125_m2_e0 | het | 92.6228 | 98.1308 | 87.7002 | 91.9195 | 1365 | 26 | 1369 | 192 | 9 | 4.6875 | |
| jlack-gatk | INDEL | D1_5 | map_siren | het | 95.7195 | 99.4730 | 92.2389 | 84.5589 | 2265 | 12 | 2270 | 191 | 11 | 5.7592 | |
| ciseli-custom | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.8911 | 98.2843 | 86.2787 | 74.9189 | 1203 | 21 | 1201 | 191 | 49 | 25.6545 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.9356 | 99.8106 | 96.1297 | 54.5329 | 4744 | 9 | 4744 | 191 | 190 | 99.4764 | |
| jpowers-varprowl | SNP | ti | map_l250_m1_e0 | * | 95.2339 | 94.6932 | 95.7809 | 91.0914 | 4336 | 243 | 4336 | 191 | 57 | 29.8429 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 91.8325 | 89.0303 | 94.8168 | 50.9778 | 3498 | 431 | 3494 | 191 | 186 | 97.3822 | |